The mouse is recognized as an important tool for generating high resolution genetic linkage maps. Multilocus probes derived from endogenous proviral sequences have been particularly informative in establishing reference loci. Such maps are useful for characterizing and mapping human disease genes because of conserved synteny and gene function between mouse and human. Oligonucleotide probes based on distinctive sequences in the LTRs of IAP elements expressed in B-cells (LS elements) react with 15-30 restriction fragments representing proviral/cell DNA junctions in mouse DNA. These oligos detect characteristic polymorphic strain distribution patterns (SDPs) in the DNAs of different inbred strains of mice, and thus provide useful multilocus probes for gene mapping. Chromosomal assignments have been established for 41 LS IAP loci by comparing their SDPs with those of known genetic markers in recombinant inbred strains of mice.